Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Sci Total Environ , IF:7.963 , 2024 Jan , V906 : P167544 doi: 10.1016/j.scitotenv.2023.167544
Deterioration of sludge characteristics and promotion of antibiotic resistance genes spread with the co-existing of polyvinylchloride microplastics and tetracycline in the sequencing batch reactor.
School of Life Sciences, Liaoning Normal University; Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.; School of Life Sciences, Liaoning Normal University; Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.. Electronic address: shishengnan013@163.com.; School of Life Sciences, Liaoning Normal University; Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.. Electronic address: 103596@lnnu.edu.cn.
With the continuous increase in microplastics (MPs) and tetracycline (TC) entering wastewater treatment plants (WWTPs) along with sewage, the co-existence of MPs and TC in the biological treatment of wastewater has attracted extensive attention. This study investigated the effect of 1 mg/L polyvinyl chloride (PVC) MPs and 100 ng/L TC co-existing on sequencing batch reactors (SBRs) (S2) treating phenol wastewater in contrast to the control with TC alone (S1). The phenol removal efficiency was significantly inhibited by the co-existence of PVC MPs and TC. Sludge characteristics were also distinctively influenced. The decreased zone sludge velocity (ZSV) and increased sludge volume index (SVI) indicated that the combined effect of PVC MPs and TC deteriorated sludge settleability, which had positive and negative linear correlations with extracellular polymeric substances (EPS) content and the protein (PN)/polysaccharide (PS) ratio, respectively. Moreover, the decreased and increased relative abundances of potential phenol-degraders and antibiotic resistance gene (ARG) carriers may elucidate the inhibition of phenol removal and promotion of ARGs propagation with the co-occurrence of PVC MPs and TC. In addition, the enhanced potential ARGs hosts, loss of the EPS protective effect, and increased membrane permeability induced by reactive oxygen species (ROS) jointly promoted ARGs dissemination in the co-existence of PVC MPs and TC. Notably, the co-occurrence of ARGs and mobile genetic element (MGEs) indicated that the co-existence of PVC MPs and TC promoted the spread of some transposase-associated ARGs mediated by horizontal gene transfer (HGT).
PMID: 37797771
Sci Total Environ , IF:7.963 , 2023 Dec , V905 : P167075 doi: 10.1016/j.scitotenv.2023.167075
Risk assessment framework for pine wilt disease: Estimating the introduction pathways and multispecies interactions among the pine wood nematode, its insect vectors, and hosts in China.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; The College of Forestry, Beijing Forestry University, Beijing 100193, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.; Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.; The College of Forestry, Beijing Forestry University, Beijing 100193, China. Electronic address: shi_juan@263.net.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: liuwanxue@caas.cn.
Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), a destructive, invasive forest pathogen, poses a serious threat to global pine forest ecosystems. The global invasion of PWN has been described based on three successive phases, introduction, establishment, and dispersal. Risk assessments of the three successive PWN invasion phases can assist in targeted management efforts. Here, we present a risk assessment framework to evaluate the introduction, establishment, and dispersal risks of PWD in China using network analysis, species distribution models, and niche concepts. We found that >88 % of PWN inspection records were from the United States, South Korea, Japan, Germany, and Mexico, and 94 % of interception records were primarily from the Jiangsu, Shanghai, Shandong, Tianjin, and Zhejiang ports. Based on the nearly current climate, the areas of PWN overlap with its host Pinus species were primarily distributed in southern, eastern, Yangtze River Basin, central, and northeastern China regions. Areas of PWN overlap with its insect vector Monochamus alternatus were primarily distributed in southern, eastern, Yangtze River Basin, central, and northeastern China regions, and those of PWN overlap with the insect vector Monochamus saltuarius were primarily distributed in eastern and northeastern China. The niche between PWN and the insect vector M. alternatus was the most similar (0.68), followed by that between PWN and the insect vector M. saltuarius (0.47). Climate change will increase the suitable probabilities of PWN and its two insect vectors occurring at high latitudes, further increasing their threat to hosts in northeastern China. This risk assessment framework for PWD could be influential in preventing the entry of the PWN and mitigating their establishment and dispersal risks in China. Our study provides substantial clues for developing a framework to improve the risk assessment and surveillance of biological invasions worldwide.
PMID: 37714356
Curr Opin Plant Biol , IF:7.834 , 2023 Dec , V76 : P102474 doi: 10.1016/j.pbi.2023.102474
How to utilize comparative transcriptomics to dissect morphological diversity in plants.
Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.; Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA; Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo Bunkyo-ku Tokyo, 113-0033, Japan.; Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA. Electronic address: nrsinha@ucdavis.edu.
Comparative transcriptomics has emerged as a powerful approach that allows us to unravel the genetic basis of organ morphogenesis and its diversification processes during evolution. However, the application of comparative transcriptomics in studying plant morphological diversity addresses challenges such as identifying homologous gene pairs, selecting appropriate developmental stages for comparison, and extracting biologically meaningful networks. Methods such as phylostratigraphy, clustering, and gene co-expression networks are explored to identify functionally equivalent genes, align developmental stages, and uncover gene regulatory relationships. In the current review, we highlight the importance of these approaches in overcoming the complexity of plant genomes, the impact of heterochrony on stage alignment, and the integration of gene networks with additional data for a comprehensive understanding of morphological evolution.
PMID: 37804608
Waste Manag , IF:7.145 , 2023 Dec , V172 : P33-42 doi: 10.1016/j.wasman.2023.09.003
Waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis promote tomato seedlings growth by benefiting properties, enzyme activities and rhizosphere bacterial community in coastal saline soil of Yellow River Delta, China.
College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China.; Citrus Research Institute, Southwest University, Chongqing 400712, China.; Weihai Academy of Agricultural Sciences, Weihai 264200, China.; College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China. Electronic address: houxin.sdau@163.com.; College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China. Electronic address: yanglong1020@163.com.
This study investigated the effects of waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis HCH2-3 on the tomato seedlings growth in coastal saline soils and chemical properties, enzyme activities, microbial communities of rhizosphere soil. Microcosmic experiment showed that the seaweed compost and rhizosphere bacteria (SC + HCH2-3) significantly alleviated the negative effects of salinity on the growth of tomato seedlings. SC + HCH2-3 amendment significantly increased the plant height and root fresh biomass of tomato seedling by 105.59% and 55.60% in the coastal saline soils, respectively. The soil properties and enzyme activities were also dramatically increased, indicating that the nutrient status of coastal saline soil was improved by SC + HCH2-3 amendment. In addition, Proteobacteria, Actinobacteriota and Firmicutes were the dominant phyla in the rhizosphere soil after adding seaweed compost and rhizosphere bacteria P. koreensis HCH2-3. The relative abundances of Massilia, Azospira, Pseudomonas and Bacillus increased in treatment SC + HCH2-3. Especially, the beneficial bacteria genera, such as Pseudomonas, Bacillus and Azospira, were significantly correlated with the increases of contents of total nitrogen, nitrate nitrogen and ammonium nitrogen in tomato rhizosphere soil samples. Consequently, adding waste seaweed compost and rhizosphere bacteria P. koreensis HCH2-3 into coastal saline soil was suggested as an effective method to relieve salt stress of tomato plants.
PMID: 37708810
Int J Biol Macromol , IF:6.953 , 2023 Dec , V253 (Pt 1) : P126558 doi: 10.1016/j.ijbiomac.2023.126558
Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress.
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China. Electronic address: bqli@mail.hzau.edu.cn.; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China. Electronic address: yxy@mail.hzau.edu.cn.
Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
PMID: 37659489
Int J Mol Sci , IF:5.923 , 2023 Dec , V24 (24) doi: 10.3390/ijms242417133
Integrative Analysis of Metabolome and Transcriptome Provides Insights into the Mechanism of Flower Induction in Pineapple (Ananas comosus (L.) Merr.) by Ethephon.
South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.; Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China.; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the 'Comte de Paris' pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering.
PMID: 38138962
Int J Mol Sci , IF:5.923 , 2023 Nov , V24 (23) doi: 10.3390/ijms242317002
Inferring the Regulatory Network of miRNAs on Terpene Trilactone Biosynthesis Affected by Environmental Conditions.
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.; Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
As a medicinal tree species, ginkgo (Ginkgo biloba L.) and terpene trilactones (TTLs) extracted from its leaves are the main pharmacologic activity constituents and important economic indicators of its value. The accumulation of TTLs is known to be affected by environmental stress, while the regulatory mechanism of environmental response mediated by microRNAs (miRNAs) at the post-transcriptional levels remains unclear. Here, we focused on grafted ginkgo grown in northwestern, southwestern, and eastern-central China and integrally analyzed RNA-seq and small RNA-seq high-throughput sequencing data as well as metabolomics data from leaf samples of ginkgo clones grown in natural environments. The content of bilobalide was highest among detected TTLs, and there was more than a twofold variation in the accumulation of bilobalide between growth conditions. Meanwhile, transcriptome analysis found significant differences in the expression of 19 TTL-related genes among ginkgo leaves from different environments. Small RNA sequencing and analysis showed that 62 of the 521 miRNAs identified were differentially expressed among different samples, especially the expression of miRN50, miR169h/i, and miR169e was susceptible to environmental changes. Further, we found that transcription factors (ERF, MYB, C3H, HD-ZIP, HSF, and NAC) and miRNAs (miR319e/f, miRN2, miRN54, miR157, miR185, and miRN188) could activate or inhibit the expression of TTL-related genes to participate in the regulation of terpene trilactones biosynthesis in ginkgo leaves by weighted gene co-regulatory network analysis. Our findings provide new insights into the understanding of the regulatory mechanism of TTL biosynthesis but also lay the foundation for ginkgo leaves' medicinal value improvement under global change.
PMID: 38069325
J Agric Food Chem , IF:5.279 , 2023 Dec , V71 (49) : P19888-19899 doi: 10.1021/acs.jafc.3c06762
Multiomics Analysis Reveals the Genetic Basis of Volatile Terpenoid Formation in Oolong Tea.
College of Life Science, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.; College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
Oolong tea has gained great popularity in China due to its pleasant floral and fruity aromas. Although numerous studies have investigated the aroma differences across various tea cultivars, the genetic mechanism is unclear. This study performed multiomics analysis of three varieties suitable for oolong tea and three others with different processing suitability. Our analysis revealed that oolong tea varieties contained higher levels of cadinane sesquiterpenoids. PanTFBS was developed to identify variants of transcription factor binding sites (TFBSs). We found that the CsDCS gene had two TFBS variants in the promoter sequence and a single nucleotide polymorphism (SNP) in the coding sequence. Integrating data on genetic variations, gene expression, and protein-binding sites indicated that CsDCS might be a pivotal gene involved in the biosynthesis of cadinane sesquiterpenoids. These findings advance our understanding of the genetic factors involved in the aroma formation of oolong tea and offer insights into the enhancement of tea aroma.
PMID: 38048088
Plant Methods , IF:4.993 , 2023 Dec , V19 (1) : P138 doi: 10.1186/s13007-023-01115-w
An efficient screening system of disease-resistant genes from wild apple, Malus sieversii in response to Valsa mali pathogenic fungus.
State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China.; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.; National Positioning Observation and Research Station of Forest Ecosystem in Yili (XinJiang), Academy of Forestry in Yili, Yili, 835100, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, China.; State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. zhangdy@ms.xjb.ac.cn.; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830000, China. zhangdy@ms.xjb.ac.cn.; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China. zhangdy@ms.xjb.ac.cn.
For molecular breeding of future apples, wild apple (Malus sieversii), the primary progenitor of domesticated apples, provides abundant genetic diversity and disease-resistance traits. Valsa canker (caused by the fungal pathogen Valsa mali) poses a major threat to wild apple population as well as to cultivated apple production in China. In the present study, we developed an efficient system for screening disease-resistant genes of M. sieversii in response to V. mali. An optimal agrobacterium-mediated transient transformation of M. sieversii was first used to manipulate in situ the expression of candidate genes. After that, the pathogen V. mali was inoculated on transformed leaves and stems, and 3 additional methods for slower disease courses were developed for V. mali inoculation. To identify the resistant genes, a series of experiments were performed including morphological (incidence, lesion area/length, fungal biomass), physiological (H(2)O(2) content, malondialdehyde content), and molecular (Real-time quantitative Polymerase Chain Reaction) approaches. Using the optimized system, we identified two transcription factors with high resistance to V. mali, MsbHLH41 and MsEIL3. Furthermore, 35 and 45 downstream genes of MsbHLH41 and MsEIL3 were identified by screening the V. mali response gene database in M. sieversii, respectively. Overall, these results indicate that the disease-resistant gene screening system has a wide range of applications for identifying resistant genes and exploring their immune regulatory networks.
PMID: 38042829
Genes (Basel) , IF:4.096 , 2023 Dec , V14 (12) doi: 10.3390/genes14122223
Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana.
Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Merida 97205, Mexico.; Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA.; CONAHCYT-Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Merida 97205, Mexico.
Fungal pathogens can have devastating effects on global crop production, leading to annual economic losses ranging from 10% to 23%. In light of climate change-related challenges, researchers anticipate an increase in fungal infections as a result of shifting environmental conditions. However, plants have developed intricate molecular mechanisms for effective defense against fungal attacks. Understanding these mechanisms is essential to the development of new strategies for protecting crops from multiple fungi threats. Public omics databases provide valuable resources for research on plant-pathogen interactions; however, integrating data from different studies can be challenging due to experimental variation. In this study, we aimed to identify the core genes that defend against the pathogenic fungi Colletotrichum higginsianum and Botrytis cinerea in Arabidopsis thaliana. Using a custom framework to control batch effects and construct Gene Co-expression Networks in publicly available RNA-seq dataset from infected A. thaliana plants, we successfully identified a gene module that was responsive to both pathogens. We also performed gene annotation to reveal the roles of previously unknown protein-coding genes in plant defenses against fungal infections. This research demonstrates the potential of publicly available RNA-seq data for identifying the core genes involved in defending against multiple fungal pathogens.
PMID: 38137044
Genes (Basel) , IF:4.096 , 2023 Dec , V14 (12) doi: 10.3390/genes14122170
De Novo RNA Sequencing and Transcriptome Analysis of Sclerotium rolfsii Gene Expression during Sclerotium Development.
Key Laboratory of Biology and Cultivation of Chinese Herbal Medicines, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China.; Hubei Engineering Research Center of Under-Forest Economy, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.; Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China.
Sclerotium rolfsii is a destructive soil-borne fungal pathogen that causes stem rot in cultivated plants. However, little is known about the genetic basis of sclerotium development. In this study, we conducted de novo sequencing of genes from three different stages of S. rolfsii (mycelia, early sclerotium formation, and late sclerotium formation) using Illumina HiSeq(TM) 4000. We then determined differentially expressed genes (DEGs) across the three stages and annotated gene functions. STEM and weighted gene-co-expression network analysis were used to cluster DEGs with similar expression patterns. Our analysis yielded an average of 25,957,621 clean reads per sample (22,913,500-28,988,848). We identified 8929, 8453, and 3744 DEGs between sclerotium developmental stages 1 versus 2, 1 versus 3, and 2 versus 3, respectively. Additionally, four significantly altered gene expression profiles involved 220 genes related to sclerotium formation, and two modules were positively correlated with early and late sclerotium formation. These results were supported by the outcomes of qPCR and RNA-sequencing conducted on six genes. This is the first study to provide a gene expression map during sclerotial development in S. rolfsii, which can be used to reduce the re-infection ability of this pathogen and provide new insights into the scientific prevention and control of the disease. This study also provides a useful resource for further research on the genomics of S. rolfsii.
PMID: 38136992
BMC Genomics , IF:3.969 , 2023 Dec , V24 (1) : P726 doi: 10.1186/s12864-023-09845-w
Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize.
School of Life Sciences, Nantong University, Nantong, 226019, China.; College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Sugar Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt.; National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, 38000, Pakistan.; Department of Biology, East Carolina University, Greenville, NC, 27858, USA.; School of Life Sciences, Nantong University, Nantong, 226019, China. bhwang@ntu.edu.cn.; School of Life Sciences, Nantong University, Nantong, 226019, China. kwang5@ntu.edu.cn.; School of Life Sciences, Nantong University, Nantong, 226019, China. jinleihan@ntu.edu.cn.
BACKGROUND: Pre-exposing plants to abiotic stresses can induce stress memory, which is crucial for adapting to subsequent stress exposure. Although numerous genes involved in salt stress response have been identified, the understanding of memory responses to salt stress remains limited. RESULTS: In this study, we conducted physiological and transcriptional assays on maize plants subjected to recurrent salt stress to characterize salt stress memory. During the second exposure to salt stress, the plants exhibited enhanced salt resistance, as evidenced by increased proline content and higher POD and SOD activity, along with decreased MDA content, indicative of physiological memory behavior. Transcriptional analysis revealed fewer differentially expressed genes and variations in response processes during the second exposure compared to the first, indicative of transcriptional memory behavior. A total of 2,213 salt stress memory genes (SMGs) were identified and categorized into four response patterns. The most prominent group of SMGs consisted of genes with elevated expression during the first exposure to salt stress but reduced expression after recurrent exposure to salt stress, or vice versa ([+ / -] or [- / +]), indicating that a revised response is a crucial process in plant stress memory. Furthermore, nine transcription factors (TFs) (WRKY40, WRKY46, WRKY53, WRKY18, WRKY33, WRKY70, MYB15, KNAT7, and WRKY54) were identified as crucial factors related to salt stress memory. These TFs regulate over 53% of SMGs, underscoring their potential significance in salt stress memory. CONCLUSIONS: Our study demonstrates that maize can develop salt stress memory, and the genes identified here will aid in the genetic improvement of maize and other crops.
PMID: 38041011
PeerJ , IF:2.984 , 2023 , V11 : Pe16481 doi: 10.7717/peerj.16481
Pharmacoscreening, molecular dynamics, and quantum mechanics of inermin from Panax ginseng: a crucial molecule inhibiting exosomal protein target associated with coronary artery disease progression.
Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India.; Department of Immunology, St. Jude Children's Research Hospital Memphis, TN, USA.; Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.; Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro, Mexico.
BACKGROUND: Exosomes, microvesicles, carry and release several vital molecules across cells, tissues, and organs. Epicardial adipose tissue exosomes are critical in the development and progression of coronary artery disease (CAD). It is hypothesized that exosomes may transport causative molecules from inflamed tissue and deliver to the target tissue and progress CAD. Thus, identifying and inhibiting the CAD-associated proteins that are being transported to other cells via exosomes will help slow the progression of CAD. METHODS: This study uses a systems biological approach that integrates differential gene expression in the CAD, exosomal cargo assessment, protein network construction, and functional enrichment to identify the crucial exosomal cargo protein target. Meanwhile, absorption, distribution, metabolism, and excretion (ADME) screening of Panax ginseng-derived compounds was conducted and then docked against the protein target to identify potential inhibitors and then subjected to molecular dynamics simulation (MDS) to understand the behavior of the protein-ligand complex till 100 nanoseconds. Finally, density functional theory (DFT) calculation was performed on the ligand with the highest affinity with the target. RESULTS: Through the systems biological approach, Mothers against decapentaplegic homolog 2 protein (SMAD2) was determined as a potential target that linked with PI3K-Akt signaling, Ubiquitin mediated proteolysis, and the focal adhesion pathway. Further, screening of 190 Panax ginseng compounds, 27 showed drug-likeness properties. Inermin, a phytochemical showed good docking with -5.02 kcal/mol and achieved stability confirmation with SMAD2 based on MDS when compared to the known CAD drugs. Additionally, DFT analysis of inermin showed high chemical activity that significantly contributes to effective target binding. Overall, our computational study suggests that inermin could act against SMAD2 and may aid in the management of CAD.
PMID: 38077444